Spatial barcodes by hydrogel lithography
AssigneeCellanome, Inc.
InventorsStephen C. MACEVICZ, Yir-Shyuan WU, Filiz Gorpe YASAR, Tarun Kumar KHURANA
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Abstract
The invention is directed to methods and systems for producing a surface coated with a plurality of spatial barcodes. In one aspect, beads carrying barcode oligonucleotides are disposed on a surface after which hydrogel chambers are synthesized around each bead and barcode oligonucleotides are released to be captured on the surface in the interiors of the chambers. Captured oligonucleotide barcodes are amplified and optionally sequenced to form a coating of spatial barcodes.
Claims21
A method of making a spatially barcoded surface, the method comprising:
- (a) disposing particles on a surface of a channel, wherein the surface is coated with primers for solid phase amplification, and wherein each particle comprises cleavably attached oligonucleotides comprising barcode sequences;
- (b) synthesizing hydrogel chambers on the surface such that each hydrogel chamber encloses a particle;
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- (c) cleaving the oligonucleotides from the particles so that the oligonucleotides are released into the chamber such that at least a portion of the oligonucleotides are captured by the primers, thereby obtaining captured oligonucleotides.
A method of making a spatially barcoded surface, the method comprising:
- (a) providing a fluidic device comprising:
- (i) a channel comprising one or more polymer precursors and a surface comprising capture elements and a plurality of particles disposed on the surface, the particles having cleavably attached oligonucleotides comprising barcodes, (ii) a spatial energy modulation element in optical communication with the surface, and (iii) a detector in optical communication with the surface and in operable association with the spatial energy modulating element;
- (b) using the detector, detecting each of the plurality of particles and identifying a position thereof on the surface;
- (c) synthesizing one or more chambers in the channel, each chamber enclosing one or more of the plurality of particles, by projecting light into the channel with the spatial energy modulating element such that the projected light causes cross-linking of the one or more polymer precursors to form polymer matrix walls of the one or more chambers, wherein the polymer matrix walls are substantially impermeable to the oligonucleotides, and wherein positions of the synthesized chambers are determined by the positions of the particles enclosed thereby identified by the detector;
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- (d) cleaving the oligonucleotides from the particles so that the oligonucleotides are released into the one or more chambers and are captured by the capture elements, thereby obtaining captured oligonucleotides.
A method of making a spatially barcoded surface, the method comprising one or more cycles of:
- (a) disposing one or more particles on a surface of a channel, wherein the surface is coated with primers for solid phase amplification, and wherein each particle of the one or more particles comprises one or more cleavably attached oligonucleotides each comprising a barcode sequence;
- (b) synthesizing hydrogel chambers on the surface such that each hydrogel chamber defines a sub-region of the surface and encloses a particle of the one or more particles;
- (c) cleaving the one or more oligonucleotides from the one or more particles so that the one or more oligonucleotides are released into the hydrogel chambers such that at least a portion of the one or more oligonucleotides are captured by the primers and copied, thereby obtaining one or more copied oligonucleotides;
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- (d) degrading the hydrogel chambers, thereby leaving the sub-regions each having attached thereto a copied oligonucleotide of the one or more copied oligonucleotides with a different barcode.
Dependencies are inferred from the claim text.